To Be a Morgenstern
by SaiyukiJ
Summary: Clary growns up with Valentine and Jonathan. This will be a mortal instruments AU, but will contain some city of bones with a twist in later chapters. There are not enough Jonathan stories in my opinion, Don't forget to REVIEW! rated m for violence, incestual feelings (nothing graphic no smut), and language in later chapters
1. Chapter 1

**Disclaimer: I do not own the Mortal Instruments**

**To Be a Morgenstern**

**Chapter 1**

**Part 1**

Valentine Morgenstern strode through his home, a tiny flailing being wrapped in a soft pink blanket held securely in his arms as he made his way to the end of the hall; towards the prepared nursery. Valentine looked down at his daughter as she started to whimper, and briefly ran his finger down the side of her face to calm her. No doubt she was hungry and tire from the long journey home.

As Valentine walked into the nursery his eyes did a quick sweep of the room to make sure it was empty before gently setting the baby into the soft mattress inside of the crib. The room had a big window, and pure pale blue walls, all the wood in the room was a dark oak, and all the metal tapestries a solid gold color. The curtains that adorned the window were the same blue color of the walls but had gold thread weaved throughout and were pulled back to show off the view of the county side.

Valentine quickly cared for his daughter, feeding her and making sure she needed no changing before laying her back down and watching her fall asleep. He quietly shut the door, and headed to his office to finish the unattended business with his comatose wife. A couple minutes later, a miniature version of the man who just left totted into the room and looked around with big dark eyes.

Jonathan Morgenstern took a long look around the room that his father had spent a majority of his time for the past two weeks. It was bright and neat, new. Jonathan shut the door quietly and took a few steps more into the room before spying the crib that sat in the middle of the farthest wall. Cautiously walking over he peeked through the bars and at the bundle wrapped tightly in a pink blanket.

Curiously, Jonathan stood as high as his little two year old legs and feet would allow and tried to see what the bundle was before it moved. Suddenly he was face to face with a pair of green eyes. Black eyes and green eyes stared at each other before the bundle moved some more, flailing its arms outside of the blanket. The baby was tiny, with thin red hair and red cheeks. Jonathan reached one of his hands through the bars and touched the baby's hand, immediately the baby gripped one of his fingers and Jonathan felt a warmth go through him.

The door to the nursery opened and Jonathan quickly took his hand from the baby, which caused a horrible wailing sound, before replacing it and turning to face the door. Valentine stood there with a curious look on his face as he surveyed the scene before him, his demon son being gentle with his angel daughter. Jonathan had a guilty look on his face, probably from being caught in a room Valentine specifically forbad him from going into.

"You know you are not supposed to be in here Jonathan," Valentine said "but seeing as how you are, I would like to meet your sister."

"I have a sister?" Jonathan asked, looking back at the baby with the green eyes.

"You do now, you are a big brother Jonathan. Do you know what that means?" Valentine asked already knowing the answer.

"No." Jonathan whispered.

"It means, you have someone to love, watch over, and protect for your entire life. She will be your companion, when she is older you will be able to play and train together, you will grow up together and share many memories. "

"What is her name?" Jonathan asked while trying to understand what his father was telling him.

"Clarissa Adele Morgenstern."

**Part 2**

The past two years Valentine had observed his children, he spent as much time with them as possible in between trying to wake up Jocelyn, his time with his other _son_, and his search for the Mortal Cup. Clarissa, or Clary as Jonathan called her, now being two was a very intelligent child for her age, she was able to read and had an exceptional skill with drawing. Valentine knew it was the extra angel blood in her system, accidentally given to her while she was still in Jocelyn's womb. It did not mean that Valentine could not enjoy the fact that he had two very gifted children.

Jonathan was a slightly different story, while he was just as exceptional as his sister he was more physical. Progressing faster physically than an average four year old. He was strong, fast, and agile which was why Valentine had decide that it was time to start training him to be a shadow hunter. The earlier he was trained the more skilled he would become, and someday his skills would be very useful to Valentine.

Although the skills of his children were a joy to observe for Valentine he found that his favorite past time was observing their interactions with each other, but specifically Jonathans reactions and interactions with Clarissa. Valentine had expected Jonathan to be watchful but distant with Clarissa, the demon in him naturally repelled by the angel in her but he was quite surprised when Jonathan took quickly to his baby sister. Keeping watch over her in the nursery when she was just a newborn, dictating to the nanny when and how Clarissa should be fed, what her bed time should be, what books were appropriate, how and how not to pick Clarissa up, what faces to make to get Clarissa to laugh. Jonathan was not only watchful over his sister, but loving, affectionate, and protective.

Valentine was astounded at the behavior Clarissa elicited from Jonathan, showing that there was more to him than his demon blood. Jonathan's behavior towards other however remained cold, he was distant with the nanny and only allowed Clarissa to touch him freely. Jonathan had no problem letting the nanny know when he was upset, and his temper could sometimes get out of hand. Once Clarissa had tripped over a broom left out by the nanny and Jonathan would have stabbed the nanny in the eye with a fork had Valentine not intervened.

To Valentine there were two different sides to Jonathan, the demon and the boy he should have been.


	2. Chapter 2

**A/N: First of all I would like to thank everyone who reviewed, followed, or favorite this FF, it means a lot to me as an author in the FF world that you would take the time to do so. Secondly I would like to set up a little more information for you the readers, about where this fic is headed. It is an AU piece where Valentine finds Jocelyn shortly after Clary is born, so Clary is raised by Valentine beside Jonathan. Everything else is pretty much cannon, Jocelyn is in a self-induced coma, Jace is also being raised by Valentine, etc. Eventually we will get into the events of CITY OF BONES but keep in mind this is NOT a Clary and Jace FF, it is all Jonathan/Clary. Also, this fic will jump ahead in time quite a bit to get the main plot points in later chapters. Also the first chapter was mainly 3****rd**** pov from valentine's end but from here on out it will be primarily from Clary and Jonathan's end. That's all for now!**

**Disclaimer: I do NOT own the mortal instruments.**

**To Be a Morgenstern**

**Chapter 2**

**Part 1**

At the ripe age of five Clary had begun to notice some things, like the fact that Jonathan and her nanny were always there but her father frequently took long and distant trips. Valentine would be gone for weeks at a time, which would have bothered Clary if it were not for the fact that she had Jonathan. Other than the times Jonathan spent hours locked in a particular room of the house, he was always with her. Clary was not quite sure what was inside the room, once she had wandered inside and caught a glimpse of lots of sharp metal objects hanging on the wall before she was thrown over her brother's shoulder and forced to sit on a chair in the corner of her room for a full five minutes ALONE. By the end of the five minutes she was crying pitifully and promising Jonathan she would never go into that room again.

"You just have to wait until your old enough." Jonathan had told her as he wiped at her face with his sleeve.

Another thing that Clary noticed was the way her father took a special interest in her drawings, Clary loved to draw and did so frequently usually keeping the drawings for herself but she gave a few to Valentine who would take them and disappear into his study for hours. Clary felt proud that her father liked her drawings so much, to the point where he would request she drawn certain shapes and pictures. Clary always did so enthusiastically and felt especially happy when her father would smile down at her work and tell her how much he liked her pictures before taking them.

Clary also noticed Jonathan's frequent mood swings and had learned when and when not to bother her brother. She was not afraid of Jonathan, had never hurt her and was always nice to her; but she had seen him on more than one occasion get angry with their nanny and during those moments she feared for the nanny. Jonathan was always caring and gentle with her but she noticed he did not show these affections toward any other member of the household, staff or their father. Although Clary found this odd, she never did comment to Jonathan about her concerns. Clary liked that her brother treated her differently, that she was special to him.

At the young age of seven Jonathan had already noticed several things, for instance his father Valentine took a special interest in his abilities and would often spend several hours teaching him to use the weapons in the weapons room. Jonathan was aware of the fact he was special, Valentine had told him on several occasions and he did his best to please his father. Even when Valentine would be gone for long periods of time he would expect Jonathan to keep up on his training and show him how much he had improved when Valentine came back. Jonathan thought it was strange that his father would spend so much time away from his children and was tempted to inquire as to the reason why but thought better of it, when his father was gone he got to spend more time with Clary.

Valentines interest in Clary was another thing that Jonathan had noticed, specifically his interest in Clary's drawings. For some reason this interest left a sour feeling in Jonathan's stomach but there was little he could do besides keep a watchful eye on Valentines interactions with her. Jonathan was well aware that be treated Clary differently but it was because Clary made him feel differently than he did with anyone else, even Valentine. While Jonathan cared for Valentine because he was his father it was not on the same level that he cared for Clary, while Valentines long absences were odd, the long hours he had to spend away from Clary to train left him feeling bitter and empty until he saw her again.

While Jonathan was not entirely sure what exactly it was he felt for his father: _fear, respect, caring_. He knew without a doubt he _loved _Clary. The time he got to spend with her was always his favorite, she looked at him with her huge green eyes surrounded by a mane of unruly curly red hair, and it always filled him a warmth he only ever got from her.

**Part 2**

For Clary's eighth birthday, Jonathan had a plan to take her horseback riding. They had both only been able to see each other in their very spare amount of time and at night when she would sneak into his room and they would spend hours talking to each other quietly. Their father had given Jonathan a stable and a horse for his tenth birthday last month, and had told Jonathan about the horse he got for Clary for her eighth last week. Valentine was currently gone on another trip, this trip was different than the rest. When Jonathan had asked his father how long he would be gone this time, his father was unsure.

"It will be a long time," Valentine had said" a month at least, the nanny will be here to watch over the estate, and I expect you to keep an eye on Clarissa while I'm gone. Make sure you both continue with your training, and give Clary the sketches of runes I left on the table. I want her to copy them down and have them memorized by the time I have come back."

"Yes Father." Jonathan replied.

Then Valentine was off, without saying goodbye to himself nor Clarissa properly. Jonathan didn't care but he knew Clary was bothered by it, she so craved affection from their father but only ever got it from Jonathan. The only time Valentine spent with Clary anymore was when he took her into the weapons room to train her to be a shadow hunter as he was training Jonathan. Jonathan would temporarily take over her training since Valentine was away, as he always did. Clary was not nearly as strong as Jonathan, but she was faster and more agile. Jonathan was better with weapons but Clary was better with runes, even though she did not have a stele yet and Jonathan did.

The brief reprieve from their training to go horseback riding was a special treat for both Clary and Jonathan. Jonathan smirked at Clary as she bounded down the stairs to the door to meet him in her boots and oversized shirt she stole from him. The rest of her ensemble was her own and Jonathan laughed at the stark contrast of combat boots, pale pink jeans, and black tee shirt, with a green hoodie over it all.

"Are you ready?" Jonathan asked her already knowing the answer from the excitement in her eyes.

"Are you kidding?" Clary asked him breathlessly before grabbing him by the hand and dragging him out the front door.

"Okay, okay slow down we have all day. You know before we ride I have to teach you the proper way to ride a horse?" He told Clary.

"I'm just so excited, we hardly ever get to go outside_. Or spend time together._" She grumbled the last bit to herself, not intending Jonathan to hear even though he did. Jonathan decided not to comment on it because there was nothing he could say to make it better.

They walked down the hill and to the white wooden stable that stood near a forest and a dirt trail. The dirt trail was the path they would ride, it was mainly out in the open and went around the stable and dipped a little in the forest before weaving back out into the open. They entered the stable and came face to face with two horses. The first was Jonathan's horse, it was all black but had light brown eyes that almost appeared gold in the light. Clary's horse was in the stall next to Jonathan's she was a pure golden color with dark brown eyes that almost appeared black. Clary gasped next to him and tightened her grip on his hand which made him smile a full smile. She was obviously happy.

Jonathan taught Clary how to care for her horse, slowly helping her get acquainted with the mare and establish a connection before they would ride. Clary mucked out the stall, brushed her pretty coat, and fed her some grains and apples as Jonathan did the same to his own horse. They spent a good couple of hours doing so before Jonathan taught clary how to saddle the horses and bring them out of the stall, they spent a couple of minutes holding onto the horse's reigns and letting them walk around before stopping and letting them drink from the water trough.

"Okay, we are going to go on a slow ride Clary. We will stay side by side and I will hold on to the reigns before I feel it's safe to let you do it yourself." Jonathan told her with a look that demanded rather than suggested she not try to argue.

Clary nodded before Jonathan helped her mount the horse, gripping the front of the horse's saddle tightly. Jonathan mounted his own horse and held tightly to the reigns of both horses before looking over at Clary and laughing out loud.

"What?" Clary asked curiously.

"You can't even reach the stirrups." Jonathan replied between sniggers.

Clary raised her chin defiantly, as she often did when feeling out of her comfort zone and glanced at Jonathan with her eyebrows raised. He flashed her a cheeky smile before instructing her to lightly kick her horse in the sides with both feet as he did the same. In no time they were both bouncing up and down as their horses began to slowly trot along the path. Jonathan had an easy time but Clary was having some difficulty hanging on, Jonathan tried hard not to laugh at the sight of her but failed. They made it all the way to the path that dipped into the woods without incident, so Jonathan begrudgingly gave Clary the reigns to her horse. Allowing her to have a better grip and not bounce around as much.

It was part way into the woods when a problem occurred, the path narrowed and Clary went first with her horse with Jonathan following slowly behind her. Something hissed and before Jonathan could do anything Clary's horse was bucking wildly and racing forward, swearing Jonathan looked down to see a snake before he forced his horse ahead. He chased after Clary as they drifted farther into the woods, eventually Clary was thrown off of her horse and fell to the ground with a thud. Ice traveled down his spine and terror seized his heart as he looked at her crumpled form.

"Clary!" Jonathan yelled. He slowed his horse down and stopped a short distance from her, hopping from his horse and running to her.

"Clary! Clary! Are you alright?!" her brother cried and turned her over. Fear causing him to tremble.

"Ow..."Clary groaned and held her left arm, she was covered in mud, sweat, and a small amount of blood from the various scraps on her arms and forehead.

Relieved but swearing loudly Jonathan picked Clary up and began carrying her back towards the stables, miraculously his horse actually followed them. Even more miraculous was the fact that Clary's horse was standing in the opening not far from the stable. . He knew he wasn't being rationale, a snake had startled the horse but he could not stop the rage that caused a white heat to travel up his body, he wanted to bash the animals head in with his fists. Jonathan glared darkly at the animal responsible for his sister's suffering before glancing down at said sister.

She was still sweating and gripping her arm, her eyes were closed and she was breathing heavily. Jonathan could tell she was in pain, and knew he had to get her back to the house immediately. Deciding he would send the nanny to put the horses away he stomped back to the house and threw the door open, laying Clary down on the couch in the living room and covering her with the throw blanket. He yelled for the nanny and she scurried to the room, he told her what happened and she immediately set off towards the stables in fear of upsetting the miniature version of Valentine.

Brushing Clary's wild mane away from her face, he ran up the stairs and to his bedroom where he retrieved the stele from his bedside table and rushing back to his sister. He quickly drew the healing rune that Valentine had taught him on her arm, wincing when she hissed in pain, and then set the stele on the table next to them.

Clary who had been surprisingly silent up until that point, exhaled sharply before opening her green eyes and staring directly into concerned dark eyes. Jonathan brushed his hand across her forehead again and down her cheek before lightly kissing her forehead.

"I think you broke your arm" Jonathan said with a tone filled with self-loathing and grief.

"Wasn't your fault." Clary whispered back.

"I never said it was." Jonathan said tersely.

"I know what you were thinking. A snake startled my horse, there wasn't anything you could have done. I still enjoyed my birthday present." Clary responded gently.

"Of course you did." Jonathan snorted "who doesn't want a broken arm for a birthday gift."

Clary looked at Jonathan for a long time while he seemed to do all he could to avoid her gaze, an amazing feat considering he was sitting on the couch next to her. Clary felt the pain in her arm dissipate and become an odd numb tingling sensation. Not knowing exactly how, Clary knew Jonathan had healed her arm and she smiled to herself before she grabbed him by the shirt and pulled him down next to her. Holding him so tight she was almost choking him, she started to laugh; finding humor in the situation that had scared her so much only moments ago and Jonathan's over reaction. Jonathan tried to pry her arms off of him but she just tightened her grip on him.

"It's not funny Clary." Jonathan said angrily.

"It is to me." Clary said through her giggles.

"Come on Jonathan, it's my birthday." She said cheekily as he glowered at her. She kissed him wetly on the cheek before snuggling into his neck, his arms came up around her automatically. He held her tightly, almost as if he was afraid she was going somewhere. It took a while but eventually the anger seemed to melt from him but his arms never loosened their hold on her. They spent what seemed like hours just holding on to each other, never even acknowledging when the nanny came back from the stables. Although Clary did catch Jonathan glaring darkly at the poor woman for interrupting their moment when she attempted to check on them. Only when it was time for dinner did they release each other. Clary went over the day in her mind and it wasn't until she snuck into Jonathan's room and they held each other tightly did she realize the real reason behind Jonathans overreaction today. There was guilt because of her injury but his true fear was losing her, Clary pulled him closer.


	3. Chapter 3

**A/N: Hello my lovely readers, A big THANK YOU to everyone who has reviewed, followed, or favorited this story so far. It makes my day to see those alerts in my inbox. I enjoy writing this story so it's nice to know others enjoy reading it.**

** = I'm glad you found this story as well. **** I could spoil the future plot for you about how Jace will fall into play in future chapters, but I won't. You will just have to be content in knowing he will eventually show up. :P**

**Silverowl1608= Thanks so much!**

**Nira Avalon= Thank you, I enjoy writing the snippets of how Jonathan would have been. I feel like if Jonathan had grown up with someone who loved him, he would have turned out differently. (Probably) Still evil cause of the demon blood but perhaps not as hell bent on destroying the world. Lol. **

**To everyone else who reviewed= THANK YOU!**

**Disclaimer: I do not own the Mortal Instruments**

**To Be a Morgenstern**

**Chapter 3**

**Part 1**

Valentine was plotting something, something big and probably dangerous but Jonathan could not bring himself to care. Valentine could put himself into danger all he wanted, just as long as he didn't try to involve Clary. However, Jonathan had a feeling that Clary was central to whatever Valentine was planning. Valentine was around a lot more than he was four years ago, and it annoyed Jonathan to no end.

The majority of Clary's time was now monopolized by Valentine, leaving very little time for Jonathan to spend with her, to counter that Valentine's own time was spent between Clary and whatever he was planning leaving him very little time with Jonathan. Jonathan was happy spending as much time away from Valentine as possible, the more time he spent with Valentine the more time he spent with the whip.

It seemed that no matter how hard Jonathan trained his mind and body, no matter how much he improved his techniques and skills from the last time Valentine scrutinized him it was never good enough. Failure in Valentines eyes was a sin and he always tried to beat the sin out of Jonathan. Jonathan was not sure what Valentine was looking for in him but he was certain he would never find it.

While waiting out his time away from Clary, Jonathan spent a majority of the time in the weapons room and library studying shadow hunter techniques and histories, downworlders (which were abominations according to Valentine), and the myths of angels and demons. He knew that angels and demons we not myths, for if they were than there would be no shadow hunters, but as far as he knew no one had seen an angel other than Jonathan Shadowhunter.

The rest of Jonathan's time away from Clary was spent terrorizing the "nanny." The nanny was never really there to watch over Jonathan, even from an early age she was uncomfortable around him so she spent her time taking care of the household and keeping a distant but watchful eye on both Clary and Jonathan. At the age of fourteen Jonathan thought it was ridiculous to keep referring to her as the nanny, Clary was twelve herself and perfectly capable without a nanny, in Jonathan's opinion. Therefore, Jonathan thought it only suitable that he make her life hell until she quit, Valentine was around more and the children were older. She was no longer necessary.

About a month ago Jonathan had taken it upon himself to start startling her from around corners, appearing out of nowhere, and staring at her intently until she was uncomfortable enough to leave the room. A week ago Jonathan started making her things in her room disappear, one thing at a time, and she noticed but said nothing. Two days ago Jonathan stood in the kitchen with her and sliced a carrot with a butcher knife, staring at her intently while doing so, and she burst into tears before running up to her room. He waited a full five minutes before following her up there and stabbing the butcher knife into her closed door.

"AY DIOS MIO" She screamed.

Jonathan laughed.

Clary was currently sitting across from Jonathan at the dinner table, their father was in the kitchen preparing dinner. Their nanny Maria had mysteriously quit yesterday; Clary was in the living room with both Jonathan and Valentine when she had nervously approached their father and as she and Valentine both went into his office to talk, Clary caught Jonathan smirking. She had asked him about it but he brushed it off. She let it go, not wanting to fight with her brother.

The nanny's abandonment meant that Valentine had to take up her work, which was why he was currently in the kitchen making dinner. Clary offered to help, wanting to learn, but Valentine told her she should not waste her energy on pointless tasks. That eventually they would have a new housekeeper and that cooking was a skill Clary did not yet need to know.

So Clary sat across from Jonathan and looked at him for the first time in what felt like weeks, but she knew it had simply been hours. Ever since Valentines long absence and reappearance four years ago, Valentine had taken her and transformed her into a young warrior. She was now more than capable of using a majority of the weapons in the weapons room, she had a lot of the runes that her father had her study memorized, she now had her own stele (a present for her tenth birthday), and she was learning a lot about the history of shadow hunters and why they were a vital race.

Clary felt proud to be a shadow hunter and she knew that eventually she would be able to put her skills to good use, killing demons and destroying downworlders. However, all this time she spent training and studying was time away from her brother and Clary hated it. Clary had on more than one occasion pleaded with Valentine to train them together but she was denied each time. Leaving her feeling hollow and numb without him.

Judging by the way Jonathan was staring at her, she knew Jonathan was feeling just as empty without her. She smiled tenderly at him and when he smiled back at her she felt warm, kind of funny, but she brushed it off.

"How was your day?" Clary asked.

"Dull, spent a majority of it in the training room today. Yours?" Jonathan asked, still smiling.

"Dull, spent a majority of it in Valentine's office studying runes. There is something I wanted to ask you about later." She replied.

Jonathan frowned as he regarded her, he himself had never been allowed to set foot in Valentine's office since he began his training. The fact that Clary had been in there, with Valentine no less made him uncomfortable for a reason he could not place. Jonathan knew Valentine was insanely proud of Clary and her runes, to the point of obsession. The obsession Valentine had with Clary's abilities made Jonathan wary and worry for his sister, if she ever disappointed Valentine would she get the whip? Had she already? Surely he would have known. The mere thought of Valentine ever raising a hand to Clary filled him with such rage that he knew that he would rip Valentine apart, slowly so that he would suffer.

Valentine came into the room with food and began serving his children, interrupting whatever conversation they would have had. Clary was filled with disappointment but she was also hungry so she dug in to her dinner ferociously, all the while attempting to be conscious of her table manners. There was no conversation to be had while the family ate, just the sound of chewing and silverware on plates.

When the food was gone, Clary attempted to ask Valentine a question about a rune she was studying but he ignored her and stalked out of the room. Telling them to put the dishes in the sink over his shoulder. Clary sighed, disappointed that he had ignored her as usual, but did as she was told. Clary never understood why Valentine took such an interest in her when he wanted her to study or train but outside of the lessons he ignored her. Clary craved affection and love that her father never seemed to be willing to give her.

Clary came back into the dining room and gathered the rest of the plates including Jonathan's, although he tried to stop her, and headed back into the kitchen dumping everything into the sink with a crash. Frustration and white hot anger filled her, she knew Valentine had no interest in her as his daughter. To him she was an object, something for him to mold and control, all he was interested in was her ability with runes and shaping her into a skilled warrior. Clary hated Valentine but at the same time she loved him, he was her only parent. Her mother had abandoned her because she couldn't stand the sight of her children, Valentine had told her the story more than once.

She felt arms wrap around her from behind and she leaned back into her brother's arms, ignoring the funny feeling in her stomach as she did so. She felt tears gather in her eyes and she quickly whipped them away with her sleeve. Jonathan set his chin on her shoulder and waited patiently for her to confide in him.

"I don't understand why he doesn't love us." Clary whispered, voice wavering. This was the first time she had ever said it out loud, somehow that made it hurt even more.

"It doesn't matter Clary." Jonathan told her quietly.

"How can you say that? It doesn't bother you that bother our parents hate us? There is obviously something wrong with us!" Clary wailed.

Jonathan turned Clary around so he could look at her, his eyes were dark and penetrating. Jonathan had always been able to read her easily and she him. He was trying to decide what to say to best comfort her.

"Maybe it not what is wrong with us, maybe there is something wrong with them." He suggested gently.

Clary took a deep breath to calm herself before laying her head on his shoulder. She wrapped her arms around him tightly and he did the same.

"I stand by what I said before. It doesn't matter that our parents hate us, or have no interest in us. We have each other and that's what matters." Jonathan told her firmly.

"That's right. I love you brother." Clary said, her reply slightly muffled by his shoulder.

"I love you too, sister mine."

**Part 2**

Clary stared at Valentine defiantly, her chin raised and her sketch book clutched tightly in her hands. Valentine stared back at her with a look, a cross between contempt and anger. He had dropped the book he was reading to her when he was startled by her outburst and slowly gotten to his feet. Clary stared up at him, a glare contorting her pretty features and an angry flush crossing her face. She was breathing heavily in her anger.

"What did you say?" He asked dangerously.

"I said 'you lying'," she replied confidently.

"I understand you are upset Clary, but I assure you that your brother is part demon. I admit that I made a mistake in giving him demon blood when he was nothing but a baby in the womb but that does not change what he is. While he is my son, he is a monster." Valentine replied slowly, as if talking to a toddler instead of the fourteen year old girl she was.

Clary stood there stunned. All her life Valentine had preached to her about the abomination of downworlders and the evil of demons. How they deserved to be destroyed. Now he was telling her that her brother, Jonathan Christopher, whom she loved more than anything in the world was part demon. A monster Valentine had said. Clary turned and stalked out of the office, leaving a shocked Valentine behind.

She walked quickly to her room and shut the door, throwing her sketchbook on the floor and tossing herself on her bed.

Jonathan himself, ran into Valentine in the hall on his way to the library. Valentine looked angry and that pleased Jonathan a great deal, he smirked slightly before whipping the look entirely off his face.

"Something wrong Father?" He asked with just a hint of sarcasm.

"No, keep an eye on your sister while I'm gone. I got a tip about the white book and am going to look into it." Valentine replied before walking past Jonathan and into the living room.

Jonathan rolled his eyes, Valentine's search for not only the white book but the mortal cup was becoming boring. He knew eventually Valentine would enlist his help but he had yet to do so, he also knew that eventually he would succeed in waking up Jocelyn. The thought of Jocelyn made Jonathans blood boil, the only good thing that Jocelyn ever did was make Clary. Valentine had taken Jonathan to see Jocelyn's comatose body on his sixteenth birthday, she was the exact image of his Clary and it upset him greatly that someone so vile could share the looks of his angel sister. Valentine had also taken the time to explain Clary's talent with runes, she had the blood of irithial in her veins while he had the blood of Lilith in his. It explained a lot. Valentine had also told him of his other _son_ Jace Wayland, or so he called himself. Living at the institute for shadow hunters, under the watchful eye of Valentine's old followers the Lightwoods.

Valentine's reasoning for this was that now Jonathan was sixteen and old enough to understand his perceptions and ideals for the world. Whether or not Jonathan agreed with them, Valentine never asked. However, it was agreed upon by both parties that Clary was not yet to know. Valentine felt she was too young and naive to understand but Jonathan simply did not want her upset. Knowing how the knowledge of their comatose mother would upset her greatly. Clary felt too much.

Jonathan went to seek Clary out, starting first in her room where he found her face down on her bed. He shut the door quietly behind him and sat down next to her form, her eyes were closed but he knew she was not sleeping. He brushed the mass of red hair from her face, ignoring the thrill that went through his body as he did.

Clary sighed and rolled over, eyes still closed, and Jonathan took the opportunity to run his eyes along her body. A wave of heat washed over his cheeks and neck, and he wanted nothing more than to run his hand down her body at that moment but restrained himself. He looked back up at her face and was slightly embarrassed to see she had been watching him, her cheeks grew pink as his eyes met hers.

"What's wrong?" Jonathan asked her.

"Valentine told me about what he did to you." Clary said, looking him directly in the eyes.

"Oh." Jonathan said in shock. Anger washed over him and he looked away from Clary in shame and guilt.

"Jonathan…" Clary said uncertainly, sitting up in an attempt to get him to look at her.

"I'm a monster, all our lives we have been told that downworlder are nothing but demons and demons are the ultimate evil. How does it make you feel that you've been living so close to one? Ashamed, angry, guilty? Maybe you would like to kill me?" He whispered harshly.

"NO!" Clary shouted before grabbing his face in her hands and forcing him to look at her. Electricity went through both of them at the contact.

"It doesn't matter to me Jonathan Christopher! It doesn't! You're my brother and I love you! It's not your fault that Valentine did that to you, he hurt you, changed your blood before you were born. I hate him but I love you. You may not have always had demon blood but you have always been my brother." Clary replied passionately.

Jonathan sat there shocked, anger was still coursing through him; he would make Valentine pay for almost ruining his relationship with Clary but he was also filled with happiness that his sister did not feel any differently about him. He loved her. Not just the normal brother sister love that was amongst all siblings; but at this moment he knew without a doubt what he had suspected since he was fourteen. He was in love with Clary.

Jonathan grabbed Clary's hands and gently removed them from his face, stoking them back and forth with his thumbs. Another blush appeared on her cheeks and she smiled at him shyly. Clary wasn't stupid, she knew that normal sisters didn't feel electricity and heat when their brothers touched them but she couldn't bring herself to care. She liked the way Jonathan made her feel.

"I love you too Clary, more than anything." Jonathan said quietly. Clary looked at him questioningly as he smiled at her evilly.

"Is that so?" She replied sarcastically, the feeling of his hands on hers making her feel warm and dizzy.

"Of course it is sister mine." He continued to smile at her with an evil gleam in his eye, he was plotting something and it made Clary slightly nervous.

He continued to look at her like that until he suddenly pulled on her hands and jerked her to him before capturing her lips with his. Clary eagerly kissed him back.


	4. Chapter 4

**A/N: Yay 23 reviews! Thank you all so much, I am so grateful to everyone who reviewed, followed, or favorited this fanfiction. This chapter may get a little confusing to those who don't pay attention but I hope not (Remember this AU). This Fic was only going to be six chapters but I might have to break it up a little more (we'll see). I went over this chapter several times before posting and I'm still not sure I'm 100% happy about it, but oh well. Thank for reading and don't forget to review!**

**Disclaimer: I do not own the Mortal Instruments.**

**To Be a Morgenstern**

**Chapter 4**

**Part 1**

Valentine sat in Magnus Banes' apartment, on the couch in the middle of an elaborately decorated room, staring straight into the golden cat like eyes of the warlock. Said warlock was staring back, face impassive stroking the head of an odd looking cat. Jonathan stood near the couch, refusing to sit, arms folded across his chest and scowling at both Valentine and Magnus. Jonathan did not like this plan for many reasons, the main reason being that Clary was the main player in whatever scheme Valentine had concocted.

"Is it done?" Valentine asked, tone careless but dangerous.

"Do you doubt me Valentine? Of course it's done, the boy and his family are oblivious to the change and will continue to be unless I reverse the spell. The Lewis family has no idea that your daughter has never been a part of their lives. As far as they are concerned Simon and Clary have been friends since they were young and in school and continue to be best friends to this day. Lucian is the owner of a bookstore here in town, and he believes that he has been involved in Clary and Jocelyn's lives since Clary was five and the _witch_ that lived below Jocelyn 16 years ago has been reliving the day Jocelyn was attacked ever since you came to me. Here is the information on the family I collected, from their address and phone number to Simon's odd habits and interests. As well as the information on Lucian. Your daughter should be well prepared."

"Excellent." Valentine said with a satisfied expression. "Don't forget what we agreed upon, you play your part, and play it well, when this is all over and I have the mortal cup you will awaken Jocelyn and the _White book_ shall be yours."

"Don't worry about me playing my part Valentine, I'm over three hundred years old and don't need a lecture. You just remember who made this all possible in the end." Magnus retorted, his face no longer impassive but daring.

"If we're settled then, how about we leave?" Jonathan drawled with a bored tone. Pushing himself up off of the wall and strutting towards the door, not bothering to wait for Valentine. The whole idea made his skin crawl, he knew Valentine had been plotting something big for years now and knew it had to do with Clary and the mortal cup but that didn't change his attitude about it. He hated the idea, Valentine for coming up with the idea, and himself for allowing him to use Clary in something so dangerous.

"I still don't understand why it has to be her and not me." Jonathan said in a seemingly carefree tone, but inside he was seething.

"I need someone who can get close to the clave, to the shadow hunters and Hodge. Between the two of you, she will come off as far less threatening and no one will suspect that something is amiss. Clary will just be Clary Fray, a girl trying to find her mom, who grew up in the mundane world with her best friend Simon Lewis and no knowledge of the shadow hunter world. You needn't worry Jonathan, your sister had been trained extensively by both of us and she has her talent with runes. She will be fine." Valentine stated in a tone that suggested he was tired of arguing and becoming angry.

This was not the first conversation Valentine and Jonathan had about the plan, nor would it be the last. It definitely was not the first time Jonathan had tried to convince Valentine not to use Clary; Jonathan tried to be discrete about his worry for his sister, trying to sound as though he was more concerned with her lack of ability to get the mission accomplished. He wasn't sure if he was succeeding or not.

They arrived home in short time and Valentine gave Jonathan the packet Magnus had gathered to give to Clary before heading to his study. Immediately Jonathan sought out Clary, finding her in her bedroom. Clary was laying on her bed, sketchbook in front of her, drawing. The outfit she was wearing gave him inappropriate thoughts, a t-shirt of his and shorts, and he quietly shut her door behind him as he entered.

He studied his sister, _and more often than not lover: ever since that first kiss almost two years ago_, and was filled with longing. Feeling eyes on her Clary turned and seeing Jonathan she quickly snapped her sketchbook shut, an embarrassed blush finding its way to her cheeks as she sat up. Jonathan handed her a package before sitting down next to her on the bed and attempting to snatch the sketchbook.

"Stop it Jonathan!" She cried as she attempted to keep it out of his reach, his arms were so long.

"Show me what you were drawing sweetheart." He smiled wickedly as he ripped it out of her grasp and flipped through it. There were many pictures of landscapes and their horses, a couple of Valentine, but the majority were of him. There were some of him as a boy to him now, some were slightly erotic but the majority were innocent, including the one she had been working on moments ago. Jonathan smiled as he looked at his portrait, it was a drawing of him sleeping with a smile on his face.

"Is this really how you see me? Innocent faced and good looking?" Jonathan asked flirtatiously.

"You know your handsome, Jonathan. Your only innocent faced when you sleep, when you are awake you look absolutely wicked." Clary said shyly.

"You don't have to be embarrassed Clary, I like that you draw me. It means you're thinking of me, apparently you think of me a lot because this book is filled with drawings of me." He teased, enjoying the way her blush darkened. After all of the things they had done together, and to each other that she could still get so embarrassed at something so simple. A drawing of him.

He looked over more of her drawings, with her beside him picking at her nails but glancing at him to see his reactions.

"I think of you too, all the time. Even when it's most inconvenient, and believe it or not a majority of my thoughts are innocent. I think of things that happened when we were young, about how much I love you, about what you mean to me. I don't like this Clarissa, this plot that Valentine has dreamt up. I don't like that you're involved and I HATE that I can't be there with you, we have no idea how long it will be before we see each other again." Jonathan sounded mournful, a pain filled his dark eyes and it captured Clary and filled her own heart with sorrow.

"It will be alright Jonathan, I will be careful and Valentine will have you so busy you won't have time to dwell on how much you miss me." Clary tried to sound teasing but the conversation was too serious in tone.

"The longest we've ever been away from each other is the two weeks it took me to secure the _white book _for Valentine. It was torture, I don't know how I'm going to survive this. We don't even know how long you're going to be gone." Jonathan said almost petulantly. His dark eyes stared into hers intensely, expressing emotions his voice wasn't. _I love you_, his eyes said, _I won't survive if something happens to you._

"Do you remember what happened after you got back? How_ hot_ it was? Just think of how amazing the sex will be after I come back." She attempted to tease again. The conversation was leaving a nasty pit in her stomach, she couldn't shake the feeling that something bad was going to happen. Instead of focusing on her own misery she was trying to get rid of Jonathan's. Bringing up sex usually worked, he couldn't concentrate on much after the topic was brought up. It seemed to help that she was wearing shorts that showed off most of her legs and a shirt that belonged to him. His dark eyes were alight with desire as they slowly looked her over.

Jonathan was battling internally with himself, he wanted to continue the conversation. Whether it was to convey how much he would miss her or to try and talk her out of it he wasn't sure. However, she was looking at him like she was going to jump him. It made his mind foggy, and he found himself unable to concentrate on anything but how she was looking at him.

He took the packet from her hands and dropped it and the sketchbook on the ground, getting up to lock her bedroom door. He turned back to face her and she was looking at him with a mix of need and shyness, her shyness astounded him. He loved her. As he approached her and climbed on top of her, he decided he would tell her all the things he hadn't yet by doing wonderfully naughty things to her.

**Part 2**

Clary sat on the cot in the cell Luke had brought her to, she took her stele out of her pocket and drew an _iritaze_ on her arm to heal the wounds Hodge's bird Hugo made. She wondered why, after everything Hodge had done to help her on her mission to retrieve the mortal cup for Valentine, he tried to convince her to leave.

_Luke _came back and together with the rest of the werewolves they went after Valentine and Jace to retrieve the mortal cup. They entered Valentine's stronghold easily enough and while Luke and his pack were busy with his followers, Clary immediately sought out her father. She found him in a room with Jace, looking at Jace Clary was immediately filled with something akin to guilt. Everything had been a ruse: the fake phone call from her mother and trashed apartment (Valentine's handiwork), the "block" in her mind (Magnus' handiwork), the feelings she had for Jace (her own handiwork). Clary was impressed with the amount of planning Valentine had put into this and Magnus' ability to not only fool Dorthea but the Silent Brothers as well. The apartment had actually been her mother's at one time, and Dorthea had been placed under a spell so that she would relive the memory of Jocelyn's attack over and over until Clary came to visit her. She was also pretty proud and impressed with herself, there were times she had wanted and almost cracked; the strain of the pretense was almost too much but in the end it had been worth it. Jace was easily wrapped around her finger and it helped that she had her "friend" Simon Lewis by her side. He made her seem all the more innocent and mundane. She had to admit that his love confession took her by surprise and threw her for a loop. She thought that maybe Magnus made the fake memories a little too strong. Everything else that had happened, Dorthea's possession and the scene at the vampire hotel had been fate or sheer dumb luck.

Clary pretended to be upset and surprised by Valentine's revelation about her heritage and how she and Jace were related, the word brother made her long for Jonathan. Valentine had confessed to Clary about Jace before she even left for the mission, all of the time he spent away from her when she was younger made sense now. Then Luke stormed in and there was a whole big scene before Valentine killed him. Once Luke was dead Valentine turned to Jace and tried to convince him to come back to Idris, but for some reason unbeknownst to her Jace seemed very reluctant. Clary was confused, all Jace had wanted was a father and now his father was standing before him. Jace was refusing Valentine's offer.

"I'm not going." Jace said definitively. "I just watched you slaughter your own Parabatai, you let me think you were dead. You never cared about me, you never loved me. The Lightwoods took me in, gave me a home and a purpose; I could never turn my back on my Parabatai. I could never leave my family."

"Very well, if you are sure of your decision I will leave you here. I want to be absolutely clear, do NOT get in my way Jace. I don't want to hurt you." Valentine said sternly, an angry and yet defeated look on his face.

"Well, if this isn't just touching." A voice that Clary would recognize anywhere drawled from a dark corner of the room. Jonathan sauntered out into the light, his arms crossed and an amused look on his face. He looked Jace up and down, as if sizing him up before deciding he was unimpressed and giving Jace a sarcastic smile.

"Jonathan, you were supposed to wait upstairs." Valentine sighed.

"Excuse me, I got bored and you know how restless I get. I decided to come and watch the drama unfold down here. I have to say, your little pet son is cute Valentine." Jonathan said all the while staring at Jace.

Clary folded herself on the sidelines, not having anything to contribute to the situation playing out, she longed to fold herself into Jonathan after not seeing him in weeks but she held back for fear of Valentine's reaction.

"Who the hell is this?" Jace demanded.

"Valentine's real son." Jonathan retorted smugly, Clary thought she saw an underlying flicker of jealously in Jonathan's eyes.

"That's enough, do you see Jace? Come with me and we could be a real family. Your brother and sister and you together at last. Fulfilling the Morgenstern legacy with the mortal cup, don't you want to be a part of the glory?" Valentine breathed. An odd gleam in his eye as he confessed his own fantasy in an effort to entice Jace to join them.

Jace looked like he was about to have an aneurism, he gripped his dagger tightly, his knuckles white and his face contorted oddly. He looked at Valentine for a long time before moving his gaze to Jonathan, who gave him another smug look, and then finally to Clary. It seemed to click in Jace's mind as he gazed at Clary's face.

"You've been a part of this the whole time, haven't you?" Jace asked her quietly.

"Yes. My name was never Clary Fray, I've never known my mother or Luke or Simon. It was all a plan to find the mortal cup, Valentine only had so much knowledge of my mother before she left him. All that we've done: infiltrating the institute, going to Dorthea, going to Magnus Banes' was all an attempt to connect the pieces. To discover where my mother had gone after she left my father, where she could have possibly hid the mortal cup, if anyone in the clave knew where she had hidden the cup. Hodge couldn't very well ask the clave, he wasn't to be trusted, nor could any of my father's other followers. It was very clever, I had not discovered that I could in fact use a rune to make a painting real until that night I showed it to you. A talent I shared with my mother and possibly would not have discovered otherwise." Clary told him firmly.

"The greenhouse?" Jace whispered, looking crestfallen.

"Even that was fake, I'm sorry if you are hurt." A guilty look must have crossed her face, Jace's own face looked a little lighter and Jonathan was giving her an odd look.

"I'm still not going with you, I won't turn my back on the clave." Jace vowed as Jonathan snorted and rolled his eyes.

"Very well, leave. I'm giving you the chance to walk away and save yourself. If you stand in our way, I will have to kill you." Valentine told him with an odd gentleness in his voice.

Jace looked at Clary once more, a mournful look in his eyes and a defeated slump to his shoulders as he walked out the door. Jonathan gripped Clary's wrist harshly and together with Valentine and the mortal cup they head back home.

**Part 3**

Jonathan was avoiding Clary that hurt her more than anything. After their return home, Valentine immediately took Clary into his office for a debriefing of everything that had happened. She told him all about the state of the institute, and the shadow hunters dwindling numbers, the accords with the downworlders as they were explained to her by Jace. Clary had expected Jonathan to be there as well but he took off to his room as soon as they set foot in the house. The way Valentine held the mortal cup was beginning to creep Clary out, she tried to ask him what his next plan of action was but he brushed off her question and sent her to bed. Not before he told her how proud he was of her and her accomplishment and grazed her hair with his hand, the only affectionate gesture he had bestowed upon her since she was small.

Clary immediately went to Jonathan's room and knocked on the door since it was not only closed but also locked, a rare occurrence indeed. He opened the door after she spent five minutes and twelve seconds continuously knocking, she counted. Jonathan stood with his arms crossed in the door way his face black aside from the arched eyebrow.

"What's your problem?" Clary spat at him. She had expected a warm welcome from her beloved brother, the time apart from him was unbearable, not a cold shoulder and an arched eyebrow.

"My problem is you, now if you will excuse me or even if you won't, I'm going to bed. I'm exhausted." He spat back as he tried to slam the door in her face. She slapped it with her hand and forced her way inside, she knew he could have easily prevented her from entering. Whether it was because he actually wanted to talk or he just didn't want to hurt her she didn't know but he didn't keep her out.

"Seriously Jonathan, what's wrong? We've been apart for weeks, I was hoping you would be a little happy to see me." She asked roughly, a lump in her throat and burning tears in her eyes.

"I am happy to see you." Jonathan looked miserable, tearful even but that could have just been because of her own obscured vision.

"You're not acting like it." She whined, tears spilling over and running down her face. She started to sob into her hands and she was deeply angry at her own inability to contain her emotions at that moment.

"I'm sorry," Jonathan sighed before putting his hands on her shoulders and pulling him towards him in a hug. "Seeing the way that _boy _looked at you, and hearing him talk to you with an intimacy that should be mine alone, I wanted to rip him apart. I don't know what happened in the greenhouse and I'm not sure that I want to but it seemed to have an effect on him, what affect did it have on you? Did you fall in love with him and get lost in your ruse little sister? You looked like you were filled to the brim with guilt."

"Of course I don't love him, it was an act Jonathan. I felt bad for using and playing with his emotions the way I did. It was easy to make him love me, to manipulate him, he was so desperate for love and I used that to my advantage. I do feel guilty, I may have damaged him beyond repair. I'm not as skilled at protecting my emotions and hiding them as you and Valentine, maybe it's our mother in me or the angel blood, I don't know. What I do know is that I love you, you are the only one for me." Clary exclaimed loudly through her sobs.

"I'm sorry, second time I've said it. I'm an ass, but I just had to be sure. I know that Valentine loves him, in a way that he has never loved me. I've heard it in the way he has talked about him in our planning and I saw it today with my own eyes. If he had that effect on our father I was not sure what affect he would have on you. I wouldn't be able to stand losing you to him. Being second best in your eyes as well." Jonathan sighed into her hair, blowing several strands of it around her face.

"You're the only one in my eyes, Brother Mine." Clary smiled up at him before stepping up on her tiptoes and kissing him harshly on the mouth. Weeks of pent up longing and hunger taking over her as she fisted her hands in his hair and around his neck, gripping him tightly to her. Trying to mold him into her, he tightened his hold on her as he responded eagerly, both of them getting lost in each other.


	5. Chapter 5

**A/N: Hello Readers, I have decided that this story can wrap up according to plan so the next chapter will be the last one. I don't want to drag out the story any longer than I have to but I may write another story similar to this one, but they grew up with Jocelyn instead. Depends on how many people are interested I suppose. Thanks so much for all of the reviews/favorites/follows! Enjoy the chapter and don't forget to REVIEW!**

**Disclaimer: I do not own the Mortal Instruments.**

**To Be a Morgenstern**

**Chapter 5**

**Part 1**

Since they had retrieved the mortal cup the Morgenstern's had been in hiding, the Clave now knew who had the cup and they were doing everything in their power to get it back. Valentine moved them from safe house to safe house every few weeks, anytime his people reported that the Clave was drawing close. The strain of being on the run was proving too much for Valentine, as he withdrew from his children and spent most of his time in his room. Frequently he would call upon Jonathan to send him out into the field, to do what Clary was unsure but he frequently returned covered in blood. Rarely was it his own.

During those times Jonathan was gone, Clary was by herself and she was feeling awfully lonely. She spent her time with her sketchbooks, trying to forget he loneliness and her unexplained guilt over the situation with Jace. She knew that she was not in love with him, that honor remained with her brother alone, but she found that she did care for him. He had gone out of his way to help her and keep her safe when he believed she was a lost shadow hunter, raised in the mundane world.

It wasn't just Jace she felt guilty about, for some reason she felt that by retrieving the cup for Valentine she was betraying the mother she never knew. It felt odd to have emotions for someone you've never met. Valentine said that Jocelyn abandoned both of her children, and that she hated them because of their blood, but the story didn't sit well with Clary. It made her anxious, like deep down she knew Valentine was lying but had neither the knowledge nor facts to prove it.

Valentine was making Clary anxious in more ways than one, the way he held the cup was creepy. Like it was his own personal life line, the only thing grounding him to the earth. Clary wasn't completely sure what Valentine wanted to use the cup for, she was pretty sure that Jonathan knew but every time she asked him about it he simply told her _ignorance was bliss, _and that he would _protect her, so don't worry so much. _It didn't do much to ease her anxiety considering he was frequently gone and she was left alone with Valentine.

The way Valentine looked at Clary now, ever since she had proven her worth to him, made her uneasy. Like she was the key pawn piece in whatever game of chess he was playing. She knew Jonathan had noticed, on the rare occasions Jonathan was home and Valentine was out of his office Jonathan would stiffen whenever Valentine's eyes were on Clary. Valentine had also had episodes of violence, she had not told Jonathan but he had thrown a glass cup at Clary once and another time raised a hand as if to slap her. It wasn't safe if Jonathan wasn't there.

Jonathan convinced Clary to take safe haven in her room when he was away, just do everything she could to stay out of valentine's way. Clary knew he was afraid to leave her alone with their father, who was becoming more and more suspicious and paranoid every day that past.

Currently Clary was in her room, sketch book in front of her, awaiting Jonathan's return. She drew picture after picture of Jonathan, and even a few of Jace, Simon, Alec, and Isabelle. She wondered if they could have been friends in another life, maybe she and Jace could have been more than that if she was raised under different circumstances.

She heard the clomping of footsteps in the hall and pass her door, she knew it was Jonathan, he was purposely walking loudly to let her know he was back and going to wash up. Minutes later her door opened and he brought her to the kitchen for dinner. Jonathan wasn't any better at cooking than Clary but he made a decent sandwich.

Ham and cheese sandwiches in front of them, they both dug in and were comfortably silent. Clary watched her brother out of the corner of her eyes and noted how tired and stressed out he looked. His normally perfect ivory hair was tousled and wet, there were purple bags under his dark eyes. Clary felt a pang of guilt again. Whatever it was Valentine was wrapped up in, he had Jonathan tangled in it with him while she was kept on the sidelines. She wanted to help her brother and take away his stress and troubles.

"Are you okay?" She asked him gently.

"I'm fine, just tired. Valentine's been keeping me busy, how have you been? Have you been staying in your room like I asked you?" Jonathan replied through a mouthful of sandwich.

"Yes, I have been keeping out of Father's way. I haven't even seen him in three days, he's been holed up inside his room just like I have." She answered.

"That's my girl. I know you don't understand everything that's going on right now but just trust me to keep you safe. I will pull you through this no matter what happens." Jonathan vowed, setting his sandwich down and pulling her head towards him to place a kiss on her forehead.

"I want to help you," Clary told him firmly, her eyes blazing with determination.

"The best way you can help me is to keep doing as I ask, Stay out of Valentines way and just trust me to see us through this." Jonathan told her with conviction, looking into her eyes to convey just how serious he was.

Jonathan knew that Clary was feeling left out of the loop, and that it was making her anxious. The amount of time he was having to spend away from her, leaving her in the clutches of Valentine, made him just as anxious if not more so. He could hold his own against the Clave, the demon blood in his veins made him stronger than the average shadow hunter and the runes on top of that made him nearly unstoppable. He slaughtered and pillaged the groups that were sent after his family, with the help of Valentine's followers, the demon in him making it an easy and emotionless task. The longer he spent away from Clary the more numb he felt, loosing himself in the battles and blood of the enemy, and becoming Valentine's hand. The emptiness he felt disappeared as soon as he saw Clary's face, and it was replaced with a warmth that only she produced in him.

He feared for her, not only because of Valentine and what he might do to her in his absence but also because of himself. His demon blood. Jonathan wasn't an idiot and neither was Clary, they both understood that normal brothers and sisters did not act and behave the way that they did with each other, nor did they fall in love with each other. But Clary and Jonathan were in love and neither of them seemed to care that it wasn't normal, that perhaps it was even disgusting, they belonged together.

Jonathan knew that it was not his blood that made him feel the way he did about Clary, for Clary felt the same way but she had angel blood, therefore it had to be fate. They were together because there was a plan for them, bigger than either of them could anticipate or understand. Jonathan was okay with that as long as he got to keep Clary. The world could go down in ashes for all he cared, as long as Clary was by his side. He was going to do whatever was necessary to keep Clary safe, even if that meant going against Valentine himself.

Valentine would fail, Jonathan knew it, and whether it was because the Clave would stop him or something else Jonathan was unsure. Valentine would fail in his plans no matter how hard he tried, he was a fool to believe otherwise, but Jonathan was not going to let him drag Clary down as well. The longer Clary spent in the dark about what was happening outside of the walls of their safe haven, the better. She could remain innocent that much longer.

Instead of retiring to Clary's room, like they usually did, they went to Jonathan's. Despite the blank white walls and sparse personal items it had a comfortable feel. However, that could have just been because they were in the room together. Jonathan's bed was made but he had some of his favorite drawings, ones that Clary had drawn for him, scattered all over the bed. Jonathan carefully picked them up and put them in a neat stack and set them on the bedside table.

He locked his bedroom door and removed all of his clothes before turning to Clary and stripping her of her own. He attached his lips to hers in a heated and passionate kiss. Laying her back on the bed he allowed her to welcome him home properly.

**Part 2**

A week had passed since Jonathan had returned home and Valentine had yet to send him away again, for that Clary was glad. Even though she was currently sleeping in her own bed, away from Jonathan, she felt safer just having him in the house.

The feeling of being watched was what arouse Clary from her slumber, she opened her eyes slowly and peered about the room. Her eyes focused on the silhouette at the door; she knew immediately it was not Jonathan, the figure didn't hold themselves right. It had to be Valentine.

"Father?" Clary whispered while sitting up, rubbing her eyes.

"Clarissa meet me in my room in five minutes," He commanded before turning on his heels and walking away.

Clary quickly got out of bed and changed out of her sleepwear. She threw on some jeans and a t-shirt of Jonathan's before she finger combed her hair. She walked quietly through the hall, the darkness and cool night air making it eerie and terrifying. The door to Valentine's room was open and so she walked in. There was a lamp on in the corner, and it gave Valentine a golden glow. Clary couldn't see his face but she knew he was studying her.

"Come with me." He commanded yet again before turning toward the far wall, next to the lamp and to Clary's great surprise started to descend downwards. Clary followed and found an open hatch door, below that were stone steps barely lit. Clary had a horrible feeling in the pit of her stomach, she was absolutely terrified, but she could see the tips of Valentine's shoes and knew that he was waiting for her to follow. Having no choice, she followed him down the steps, and into what appeared to be a cellar. There were candles and lamps all over the room, but somehow the room was still dim. There were various wooden tables around the room, and what looked like chemistry equipment. _So this is where Valentine disappears _Clary thought.

On one wall there was a large wooden door, and Clary wondered what was behind it. She was afraid she was going to find out. Besides the tables there were also a couple of wooden chairs and a set of what looked like doctor scalpels and knives. Clary looked back at Valentine warily, his back was to her and he was taking something out of a leather bag. Clary considered bolting towards the stairs, running to her brother, but she was terrified. If she did not go along with what Valentine was doing, he was going to hurt her; of that she was absolutely certain. If she ran to Jonathan he would hurt her brother as well, his scarred back was proof of that. Would Jonathan take his punishment willingly or stand up to their mentally unstable father?

"Sit down on the table Clarissa," He told her without looking at her. She walked over to the wooden table closest to her and perched herself on the edge, trembling.

Valentine came around her and tied a thick elastic band around the bicep of her left arm, he then took out a syringe and jabbed her in the arm. Drawing some of her blood, she cried out as the needle pierced her skin. Valentine was not gentle. Clary tried to stop her shaking, to prove to herself and Valentine that she was not going to let him scare her, but it did not work. Her breathing turned harsh as he took the syringe and walked over to his bag, he appeared to be emptying its contents into a cylinder container.

He took another cylinder container out of the bag, this one already had something inside of it. It was a red liquid but appeared to glow, as Valentine brought it closer she noticed that it did in fact glow but it also had specks of gold inside.

"Do you know what this is Clarissa?" Valentine asked her, scrutinizing her reactions.

"No," She answered quietly.

"This is the blood of Ithuriel, blood that runs through your veins. When your mother was pregnant with you, I had no idea. To make a long story short I thought your mother was sick with depression so I fed her some angel blood to make her better, you were in her womb at the time. This blood flows through you, gives you're the gift you have with runes. I only gave her a little bit of angel blood, do you know what gifts you could develop if you had even more of his blood?" Valentine asked her with a sadistic smile on his face. He was waving the container in front of her face, taunting her with the probability.

"What I did to Jonathan was a mistake, demon blood was too unpredictable. Jace has some of Ithuriel's blood in him as well but he is no soldier, he feels too much. You, my daughter, I have raised you from birth to be one of the finest warriors to grace the realm. You have had Ithuriel's blood in you since before you were born, I lost six years with Jace and perhaps that is why he could never be the weapon I need him to be. However, I have you and I will continue to command and shape you into the perfect weapon." Valentine continued.

"NO!" Clary gasped.

"There is nothing you can do about it my daughter. You are my blood, I made you and I will do with you as I please." Valentine spat. He grabbed Clary by the hair and dragged her off of the table and into a chair, he grabbed her left arm and pulled it across the side of the table before drawing a knife from his belt and stabbing it into her hand. Pinning her to the table, Clary cried out in pain and tears stun her eyes.

Valentine grabbed Clary's face with one hand and tried to pry her mouth open, which Clary stubbornly was trying to keep closed, and held the container with the other. Clary fought as best she could, kicking and striking out at her father while her left hand was pinned to the table. She tried to shake her head back and forth but his grip was strong and bruising.

Valentine set the container against Clary's pursed lips, and held her face still by gripping her under her jaw, bordering on her throat. Cutting off her air way and choking her, Clary knew she was going to lose this battle.

"GET THE HELL AWAY FROM HER!" an angry voice bellowed, the sounds echoing in the cellar.

Jonathan stood at the steps of the entry way, a ferocious expression on his face and his hands clenched into fists. He looked as if he had woken up only moments ago, he was still in his sleepwear and his hair was a mess. If looks could kill. Valentine's gripped loosened and the container was lowered but Valentine still held onto Clary's jaw.

"This doesn't concern you Jonathan, go back upstairs and go to bed. Leave me and your sister be." Valentine told him firmly.

"The hell I will, now back away from her," Jonathan spat, coming closer to the pair. "I've always known you were a sadistic, power hungry bastard. Look at what you did to me, but to continue to use your own children as experiments brings your morbid fascination with power to a whole new level."

"I don't want to have to hurt you Jonathan, but if you do not do as I say I will get out the whip." Valentine retorted harshly, eyes trained on Jonathan with wariness that Clary had never seen on her father. As Jonathan approached slowly Valentine lowered the container completely and resealed it, grabbing the knife that was pinning Clary to the table he ripped it out. Clary let out an anguished cry and fell off of her chair and to the ground, clutching her bleeding hand to her chest.

"You don't want to stand in my way Jonathan, think of all that Clary could do with more of Ithuriel's blood. The runes that could be created or who knows what other power she could have. She will be my assurance that my plan will not fail, that _our_ plan will not fail. She will be our secret weapon against the Clave and together the Morgenstern family will get the blessings of Raziel and create a new race of nephilium." Valentine said with conviction, holding the knife tightly in his hands, prepared to use it if necessary.

"I don't care about blessings from Raziel or the glory of the Morgenstern name, I just want Clary safe. You have no idea what more of Ithuriels blood will do to her. I won't let you use her in your twisted plan for power." Jonathan stated with just as much conviction.

Jonathan had moved so that he and Valentine were face to face, only about a foot apart. Clary watched them apprehensively, not knowing what was going to transpire between the two.

"You would turn your back on your father? Your creator? What could bring you more satisfaction than bringing the Morgenstern name back to its rightful place of glory? Your sister? You're a demon Jonathan, it's in your nature to destroy not to protect." Valentine scoffed.

Jonathan glared at Valentine, it was a look of pure hatred. The look startled Clary, she knew there were bitter feelings from Jonathan about their father but Clary had no idea how bitter the feelings actually were. Jonathan hated Valentine.

Valentine took Jonathans silence and glare as his answer and struck out with the knife, aiming for Jonathan's shoulder. Jonathan was quick, faster than Clary had ever expected, and he dodged the knife easily. Jonathan grabbed the arm Valentine had used to strike out and slammed him into the ground. Valentine coughed violently, coughing up blood and dropping the knife before Jonathan kicked him in the face. Effectively knocking him unconscious. Jonathan brought his foot back up, presumably to kick him again but Clary gasped out his name.

Jonathan whipped his head around and stared down at her for a moment before grabbing her roughly and throwing her over his shoulder, heading up the cellar stairs. He shut the hatch door and pushed Valentine's chest of drawers on top of it with one hand. He headed down the hall to his room and set her down gently on his bed, grabbing his stele and drawing a quick healing rune on her bleeding hand.

He started grabbing bags and items and throwing them into the bags, Clary was confused for a moment before she realized he was packing.

"Go to your room and start packing anything you want to take with you, we are leaving." Jonathan told her without looking up from his own packing.

Clary quickly made her way to her room and opened her closet, she found several bags inside that she knew had not been there before. Jonathan had apparently been planning to leave. She quickly started to pack, her clothes and toiletries, a couple of personal items, and her sketchbooks and art supplies. Grabbing all of her bags she ran back to Jonathan's room and he was there waiting for her, ready to go and looking anxious.

"Where are we going?" Clary asked tensely.

"Somewhere safe, don't worry I'm going to take care of you. I won't let Valentine hurt you." Jonathan answered with a sigh, his breathing harsh with anticipation and worry.

He grabbed her hand and his bags and they headed out of the house, once outside he and Clary took one last look at the house they had grown up in. Then Jonathan pulled out his stele and drew the rune Clary had taught him, they held hands tightly as they jumped into the portal. Jonathan let his mind drift off of their desired location and back on his sister as they came through the portal. They landed harshly, Jonathan made sure Clary landed on top of him, and held each other for a moment. Their eyes never left each other's as their lips connected and they both breathed a sigh of relief. Clary stood up first and looked up at their location with confusion. Jonathan knew he would need to explain exactly what his plan was before they could set foot inside, how he had been planning this escape for months and what their next course of action would be. He stood up and grabbed her hand, lacing their fingers together. He let his gaze drift from his sister and onto the front door of the institute.


	6. Chapter 6

**A/N: Hello my Lovelies! Okay, I fibbed a little in the last chapter. After I sat down to write the last chapter it turned out to be rather long. So I split it into two chapters. Thank you all so much for your reviews and alerts for this fic! It really does mean a lot to me. So Sorry for any spelling or grammar mistakes. On with the Story!**

**Disclaimer: I do not own the Mortal Instruments, also I have no money so please do not sue.**

**To Be a Morgenstern**

**Chapter 6**

**Part one**

Needless to say their arrival at the institute was not welcome by anyone except for Robert Lightwood. He and Jonathan seemed to have an understanding of sorts, Robert was the one who made everyone lower their weapons. Upon entering the institute we were immediately met by the crack of a whip, a blade at Jonathan's throat, and a knocked arrow. Jonathan shoved Clary behind him, never letting go of her hand and giving it a reassuring squeeze.

Robert quickly made his way into the foyer of the institute and calmed everyone before escorting Maryse, Jonathan, and Clary into the library to talk. Everyone else was dismissed to their rooms, Jace shot Jonathan a look full of hate as he went, ushering a little boy in front of him.

"I thought you weren't coming for another two weeks." Robert stated to Jonathan as he shut the library doors. Jonathan ushered Clary into a large cushioned chair by a bookshelf and set himself on the arm, still holding her hand tightly.

"We had to leave earlier than expected, Valentine was trying to poison Clary. I walked in on them after I heard Clary scream." Jonathan told Robert, glancing at Clary to gage her reactions.

"What was he attempting to poison her with?" Maryse asked, the first time she had spoken to either of them.

"I knew he would try it eventually, he was attempting to give her more of Ithuriel's blood. He accidently administered it to her when she was still in Jocelyn's womb, and because of the blood Clary has a significant talent with runes. I guess Valentine wanted to see what else Clary would be able to do if she had even more angel blood." Jonathan was attempting to keep calm for Clary's sake but she could see the underlying anger, it was almost throbbing beneath his skin.

"It took me years to see how twisted Valentine really was, I never would have thought that he would go to such extremes. Trying to poison his own children?" Maryse looked sick, her pale skin taking on a green tint.

"It will be okay Maryse. Valentine has an incredible ability to charm and manipulate people to get what he wants, we were no more fools than the rest of the Clave. Jonathan, from what you have told me and what you have seen, do you think Valentine will attempt to bring his plan into fruition soon?" Robert asked while laying his hand upon Maryse's shoulders to calm her.

"I do, Valentine has the foolish idea that he will rid the world of downworlders and all that ally with them. He wants to create a brand new league of Shadow Hunters, in which he will lead, by summoning the angel Raziel. He already had the Mortal Sword when we helped him retrieve the Mortal Cup, so there is nothing stopping him from summoning Raziel now. I believe he wanted to see what would happen to Clary so that he would know what power he wanted Raziel to bestow upon him." Jonathan told them quickly, Clary sat listening intently; she had no idea that any of this was going on. Clary thought he wanted the Mortal Cup to make more shadow hunters and lead them, like he was going to with the Circle, not create a brand new race and commit genocide.

"That's not true, we will stop him." Robert told Jonathan firmly, "Wasn't that the point of you contacting me in the first place? To inform the Clave so that we could all work together to stop Valentine and preserve our world?"

"You're right Lightwood. However, I highly doubt that the Clave will be willing to work together with me. I was Valentine's hand for years after all." Jonathan told him while wearing his signature sarcastic smirk.

"I don't hold that against you Jonathan, and after speaking with several members of the Clave; I don't think they will either. The two of you were raised to believe outrageous lies by an insane power hungry man, it's all you've ever known. The fact that you are here now speaks a lot to your values, we will do all we can to stop him." Robert replied, Maryse was looking at them both with something akin to pity in her eyes.

"Don't give me too much credit, my reasons for coming to you are entirely selfish. I could care less if the world went down in ashes, I'm part demon after all, but I know that Clary cares. Clary cares too much and I care for Clary. That is the only reason I am here right now." Jonathan told him with a cold glare, daring Robert to try and find some piece of good in him.

"Well, whatever your reasons, we need to come up with a plan."

Robert and Jonathan had both asked Maryse to find somewhere for Clary to sleep, Clary hadn't even realized she was nodding off until Jonathan shook her shoulders lightly. Maryse didn't look to happy to be left out of the planning but she escorted Clary to a room anyway. The room was finely furnished, and there was a king sized four poster bed with navy blue bedding in the middle of the room. The bed looked extremely inviting in Clary's exhausted state, she was almost too exhausted to care that Jonathan was still leaving her out of the loop.

"He wouldn't tell me very much about what happened between the two of you, but I know that the time he spent with you impacted him a great deal. Before you came he was reckless, selfish, and arrogant, he didn't care about others feelings or have the ability to feel sympathy for others. Isabelle told me that having you here changed him and then when you left again, it's like he's hollow." Maryse said very quietly, afraid of who might over hear.

Clary didn't need her to specify which HE she was referring to, she knew Maryse meant Jace. Clary felt that pain of guilt seep back into her and she felt tears in her eyes, but she would not cry; she didn't deserve to cry or show weakness in front of this woman, she knew how badly she had hurt Jace. Suddenly she was wide awake, Maryse was studying her and Clary wasn't sure what she was looking for but apparently she found it because she nodded her head lightly and closed the door on her way out.

Since Maryse was gone, Clary allowed a few tears to leak out of her eyes. It wasn't because of the guilt she felt about Jace. Her whole world had come spiraling downwards in a matter of moments. She had always known her father didn't love her but she never thought he would go to such drastic measures as to change her very being. Clary thought she was done being his experiment.

For some reason Clary did love her father, she hated him as well but he was the only parental figure she had in her life. If not for Jonathan she would have no one. Clary laid down of the bed with a huff and wiped at her eyes angrily, curling up into a ball she waited for sleep to take her.

**Part 2**

As the darkness lessened around Clary and she slowly became aware of what had woken her up, she felt a feather light touch on her cheek.

"Clarissa Fray, wake up. I want to talk to you," A voice she knew belonged to Jace whispered.

"What are you doing?" Clary asked groggily, brushing his hand away gently and sitting up to face him, he was crouched next to the bed. His golden eyes looking into hers.

"I followed you and Maryse as she brought you here, like I said I wanted to talk,"Jace told her.

"So talk," Clary said but tried to make her tone gentle and soothing.

"I don't blame you for what happened with the Mortal Cup," Jace surprised her. "I remember what it was like to grow up with Valentine, hell six years ago he abandoned me and I still follow the rules he ingrained in me. Even though I now know he isn't really my father, I still find myself thinking about the lessons he tried to teach me. My point is that, he really is your father; for the past sixteen years he has ingrained the very same lessons into you. How can I blame you for that?"

"I didn't know what he was planning to do with the cup, I thought he wanted to create more shadow hunters. Not become a dictator," Clary said sadly.

"I know. It will be okay Clary."Jace tried to comfort her which brought on a whole new wave of guilt.

"Don't do that," Clary practically spat. "Don't try to comfort me, not you, I don't deserve it."

"I know, I understand why you did what you did. It doesn't change anything, I have feelings for Clary Fray but I don't know you Clarissa Morgenstern. I would like to, we're the same you and I. We both have the blood of Ithuriel running through our veins. I kept running the time we spent together in my mind after you left, even though you were pretending to be someone else I still think I got to see glimpses of the real you. Like in the greenhouse before we kissed and in the vampire hotel." Jace told her gently.

"I like you Jace, I really do. I feel awful about what I did to you but-"Clary was cut off as the door to her room opened and Jonathan was standing in the doorway.

"What are you doing in here Jace Wayland?" Jonathan demanded.

"Just having a chat." Jace answered with a smirk, shrugging as he stood and made his way to the door. They sized each other up, both sons of Valentine, and Clary was surprised to see how alike they were in the way they held themselves. Jonathan was taller but Jace was broader, Jonathan was dark and Jace was light, Jonathan's smirk held a sinister air and Jace's held an arrogant one. Jace passed Jonathan and looked back at Clary mouthing _later_ to her before strutting away. Jonathan kept his eyes on Jace as he left and stiffened when he saw what Jace mouthed. He slammed the door after Jace made his way down the hall and turned to face his sister. He looked angry, his normally pale cheeks held a rose tint to them and his eyes almost sparkled with malice. Clary felt a sliver of fear creep up her spine, she had never seen him like this before, so openly hostile.

"What was he doing in here?" Jonathan seethed.

"He wanted to talk," Clary offered gently, trying to calm him. Although her own ire was starting to come to a head.

"I don't like him talking to you!" He shouted, his dark eyes wide and his breathing becoming labored.

"Jonathan, stop!" Clary shouted back, she never raised her voice at Jonathan and hardly ever lost her temper. The fact that she was doing both shocked him and he paused. Jonathan took her in for a moment, her face was red and her hands were clenching and unclenching, her mane of hair seemed to crackle, and her eyes sparked fiercely.

"You stay away from him Clarissa," Jonathan demanded, but with a softer voice.

"DON'T TELL ME WHAT TO DO! YOU ASSHAT!"Clary screamed. " YOU WONT TELL ME ANYTHING THAT'S GOING ON, YOU SEND ME TO BED LIKE A CHILD. IM NOT A CHILD AND YOUR NOT THE BOSS OF ME, IM MY OWN PERSON AND IF I WANT TO TALK TO JACE THAN I FUCKING WILL!"

Clary was aware that she was behaving irrationally, she shouldn't be talking to her brother like this; but she was so worked up over the events that started since Valentine woke her up that she didn't heed the rational part of her brain. The more she screamed the Angier she got and by the end of her tirade she had flung herself off of the bed and toward Jonathan, catching him off guard and knocking them both to the floor.

Her fists were flying as she pummeled Jonathan with all she had, he held up his hands in front of his face to keep her from doing any real damage. Somewhere in the middle Clary started to sob and the fight in her dissipated, making her slow her attack on her brother until she stopped all together. Collapsing on top of him, she started shaking and sobbing uncontrollably. Jonathan's hands quickly came around her after her outburst and he held her to him tightly.

Clary woke up, again, to the feeling of someone stroking her face. Instead of opening her eyes to see tawny gold irises she was looking into the deep dark depths of her brother's. He was holding her gently while they faced each other, and he smiled at her gently as he stared back at her.

"Feeling better?" He asked her.

"I'm so sorry,"Clary whispered, ashamed at the attack on her brother. He had saved her from Valentine, protected her all her life, and this was how she repaid him?

"Don't be, I know you were just frustrated and scared. I have been keeping you out of my plans and it hasn't been fair to you. Maybe if I had told you what was going on you would have come directly to me when Valentine woke you up instead of following him to the basement." Jonathan whispered gently, tilting her head to look him in the eyes.

"I'm still sorry, and grateful, thank you for saving me." Clary reached up to brush Jonathan's own hair.

"Robert got word last night that Valentine wasn't at the house, the cellar door was busted off its hinges and the chest of drawers in shambles; Valentine got himself out of the house. We think that he is going to go through with his plan to summon Raziel. I believe he wanted to see what would happen to you if you had even more angel blood so that he would know what to request of Raziel. He doesn't just want to reform the Clave, which may have been his intention when he was young but not anymore. He wants to create a new breed of Shadow Hunters, one that he can control and have complete power over. With his new army he will defeat the Clave and destroy the downworlders" Jonathan explained.

"There's something I have to confess, I have always know of his plan to create new Shadow Hunters. He has never kept his intentions from me, he needed me as his hand. He never told me of his intentions toward you, but I could assume. I was perfectly content to let him burn down the world as long as I could keep the two of us safe, but that was before Valentine really took an interest in your talent with runes. After I noticed how much attention Valentine started to show you, I became wary and suspicious. I think that if Valentine had known how much you mean to me he would have hid his interest better, but to him I was a demon. I couldn't love anyone let alone my own sister. "Jonathan told her quickly, his eyes pleading with her to just listen.

"Once I became fully convinced that his intentions were to use you as an experiment, a weapon of sorts, I immediately came into contact with some of his old followers while on my errands for Valentine, after we retrieved the Mortal Cup. The Lightwoods were initially uneasy but after some convincing and details they agreed to help me stop Valentine. I also have a current follower of Valentine's working as a spy of sorts. No one wants to live in a world where Valentine is ruler. We had a plan in place, you and I were supposed to come to the institute next week, but after last night I had to improvise." Jonathan finished.

Clary was shocked, and at the same time she was unsurprised. She was not aware that Jonathan had thought this through so thoroughly and that he had been planning to stop their father. She was aware of the fact that Valentine confided in Jonathan so completely. Valentine's biggest flaw was assuming that he had control over Jonathan, like he could be controlled. The sliver of fear was back, Valentine had escaped the cellar and could be anywhere. He was probably looking for her and her brother.

"So what are WE going to do?" Clary emphasized.

"WE are not going to do anything. You are going to stay here at the institute with Maryse and Magnus Bane while Robert and I form a team to stop Valentine." Jonathan told her while smirking, her attempt to include herself was adorable; as was the scowl she was currently directing at him.

"I want to help. I want to help stop Valentine, I need to help stop Valentine." Clary said fiercely.

"No, you need to stay here and let me handle it." Jonathan told her, trying to keep the conversation from turning into another argument from last night.

"What the fu-!"

"Language Clarissa!" Jonathan said sternly as she jerked herself up into a sitting position. She looked at him with bright eyes, pleading with him to let her help. Jonathan just couldn't put her in that kind of danger.

"Trust me." Jonathan kissed her on the forehead. He got up and gathered some clothes from his bags, and his gear. He changed quickly, chuckling loudly when he turned and saw Clary staring at him with a bright blush on her cheeks. So little time.

Walking back over to her he kissed her deeply, pouring all of the emotion he had dwelling within him into the kiss. She gripped his shoulders tightly, pulling him into her and attempting to pull him on top of her. So little time.

"I love you," He whispered against her lips fiercely." I promise I will be back soon, two days tops. I will stop our father and make him pay for what he tried to do to you. Promise me that you will stay here, and stay safe. If something happens, promise me you will put your talent to use and protect yourself."

"I promise. Just please be careful and come back to me." Clary said quietly "I love you too, more than you know."

Maryse had taken her to drink tea about an hour after Robert and Jonathan left to meet members of the Clave. Jace, Alec, and Isabelle had gone with them. Clary was unsurprised to see Magnus Bane sitting at the table waiting for them, his glamourous appearance was unmarred by the sour look on his face. He straightened in his chair when he caught her eye and his face went blank.

Tea had been quiet and awkward, Magnus and Maryse seemed to make conversation easily enough but Clary found it hard to talk to them. What did they think of her, Valentine's daughter? To their credit they did try and keep her in the conversation and included.

Clary dismissed herself after about forty-five minutes, telling Maryse thank you and giving Magnus a soft goodbye. On her way to her room she let herself get lost in thoughts of Jonathan, Jace, and interestingly enough Simon. She wondered how the mundane was doing and if his memory had been restored to normal. Did he remember her? She found herself missing the fake friend, could they have been real friends in another time?

She was so caught up in her thoughts that she didn't sense the presence behind her until he was standing an inch away and had his hand wrapped around her throat. She was being dragged and sucked into space, the hand around her throat accompanied by a hand around her waist in a tight hold.

Then they were gone.


	7. Chapter 7

**A/N: Hello my lovely readers! Well, here we are the last chapter of TBAM…I may cry. A BIG thank you to everyone who has reviewed/favorite/followed this story, it makes my day to see that in my inbox. I still have not decided whether or not I will write a parallel to this story: same pretense except they were raised by Jocelyn (To Be a Fray). I am waiting to see if anyone is interested and if I feel up to the task. If I do write the parallel it will feature more Jace but will all around be a Clary/Jonathan shipper. Probably longer with more angst as well but at the same time a bit lighter. Anyway, let me know if you're interested in "To Be a Fray."**

**Disclaimer: I do not own the Mortal Instruments, also I have no money so please do not sue.**

**To Be a Morgenstern**

**Chapter 7**

**Part 1**

Clary woke up to the sight of a lake and her own wet hair, she felt a tight grip around her ankle and herself being dragged through sand. Clary tried to raise her hands to grip the sand and stop herself but found that her hands were bound together. She came to a stop suddenly and the grip left her ankle, looking down she saw Valentine. He was smiling at her, but it was not the kind welcoming smile a father would give his daughter. His smile was evil, like a predator who decided he was going to enjoy torturing his pray before devouring them.

Clary tried to scream but found that her voice was gone, and after trying to sit up, that her feet were also bound. Valentine moved away from her to start a fire on the beach, the light giving his hair a luminescent glow.

"I've had to revise my plans a bit," He confessed. Finished with the fire and moving to a bag not far away from her. "I used the rune you created to make a portal and bring you here. Since you and your brother's betrayal, I have decided that experiments are too unpredictable. So you can relax, I am not going to experiment on you. Instead I need a sacrifice. You should be honored, becoming a sacrifice for your father is a privilege I offer only to you."

"I will become the next Jonathan Shadowhunter, and the Clave and down worlders alike will fall to my feet. If I have to kill you, Jonathan, and Jace then I will do so. I had no idea that you and Jonathan had become so close, for him to betray me, he must love you. I didn't think that he would ever be capable of such an emotion, obviously I underestimated him. That's twice now you have taken those I love away from me Clarissa Adele. There will not be a third time." At Clary's look of confusion he continued, dropping to his knees to look her in the eyes.

"Your mother discovered she was pregnant with you and she betrayed me. She was planning to take Jonathan with her but I couldn't let that happen, so I faked our deaths. She made off with the Mortal Cup and you, went into hiding. She changed her name to Jocelyn Fray and hid the Mortal Cup, I finally found her after she gave birth to you. Her precious Clarissa Adele Fray, she left to protect you. You are the only thing she has ever loved more than me and for that I have always hated you. I can tell by the look on your face you are mortified. Don't fret, I didn't kill her. I love her, even if she betrayed me. She put herself into a magically induced coma to protect the cup, she's been in my care ever since." His eyes strayed to a figure lying far away from them, it was too dark for Clary to see anything more vibrant red hair.

It was her mother, Jocelyn.

The very idea that the woman who gave birth to her was lying only feet away brought forth so many emotions Clary wasn't able to process them. She forced the tears out of her eyes and focused back on Valentine. He had moved back to the bag and was pulling items from it, she recognized the cup immediately and the sword. He then began to draw runes in the sand, a feeling of dread washed over Clary as she realized she was about to die.

She had no idea where Jonathan or the rest of the Shadow Hunters were, her mother was completely comatose, and she was unable to help herself.

She was going to die.

Valentine came towards her with a sword, holding it tightly in one hand and striding towards her with intent. He flipped her on her back and gripped the hilt with both hands, the point of the sword resting on her chest above her heart; before raising it swiftly and like a flash of lightning bringing it back down.

The sword went flying from his hands before it reached her and he stood there shocked for a moment before looking to the right, above Clary's head. There was Jonathan, his own sword held tightly in his hands, bloody and glorious looking.

"Clary, are you hurt?" Jonathan asked while looking Valentine in the eyes.

She attempted to answer but still couldn't speak, above her own garbles she heard Valentine tell Jonathan he had placed a quietude rune on her.

"You don't want to do this Jonathan." Valentine tried to sound persuasive.

"Join me, and then you, me, and your mother can be a family and restore the Morgenstern name. We will reform the Clave and rule a brand new generation of Shadow Hunters. The angel will bestow glory and blessing onto our name." He said in that same silky persuasive tone.

"What about Clary?" Jonathan asked, his hands never wavering from his sword.

"What about her? What is one life to eternal glory, son? I admit this is hard but the honor that has been given to Clary, the taking of her life will bring forth Raziel and therefore our Morgenstern legacy. She is playing a vital role in our restoration." Valentine looked uncomfortable, like he didn't want to over analyze his own reason for sacrificing his daughter.

"You power hungry bastard! You would sacrifice the life of your own daughter? Do you not realize how sick that is? How twisted and depraved? No wonder Jocelyn left you." Jonathan spat.

"Jonathan, please put down the sword. We can discuss this like rational adults and I'm sure we can come to an understanding. What would your mother think? Seeing the blood thirsty look you have in your eyes? Do you really want to do this in front of Clary or her?" Valentine turned his head to look at Jocelyn and Jonathan followed his eyes, his face paling and hands going limp when he spied his mother on the ground.

The momentary distraction proved to be enough and Valentine pulled a dagger out of his belt, stabbing Jonathan in the heart. Jonathan gasped in surprise and pain as his eyes stared back at Valentine confused. Jonathan's sword landed with a thud in the sand as he collapsed to his knees and his father's arms. Valentine held him closely, and fell to the ground with him.

"I'm sorry my son, I guess the honor goes to your instead." Valentine said gently, trying to soothe the now dying Jonathan.

Jonathan gasped a few more times, his hands gripped onto Valentines shirt tightly before they went limp completely and his arms fell to his sides. Valentine pulled the dagger from his heart, now wet with his blood, and gently lowered his body to the ground. Valentine shut Jonathan's eyes, whispering something quietly.

He then turned back to his cup and sword, walking towards the runes in the sand and lake. Clary wasn't sure what he was doing, and at that moment she couldn't care. Jonathan was dead. She turned her body towards him, and slowly crawled to his body. She laid her head on his chest and allowed a few tears to leak from her eyes.

Valentine could kill her now, she had no reason to live.

The thought made her angry.

Valentine was chanting words Clary couldn't understand and doing something weird with the sword and water of the lake. Determination suddenly filled Clary, Valentine wouldn't win. She would stop him in honor of Jonathan and then she would die. She would die with her brother, her love.

With difficulty she managed to pull her stele out of her belt and crawled slowly to the runes. She didn't recognize very many of them but one she did. She made her mark over that one and waited. The runes started to glow brightly and all of the sudden a bright light appeared, and from that light came Raziel. Valentine had succeeded in summoning the angel.

The angel Raziel was talking to Valentine and it seemed angry, scolding Valentine for all the evil he had done and then having the audacity to summon him. Valentine's pleas and explanations fell on deaf ears as the angel suddenly pointed to the runes and Valentine turned to look at them. The rune that held Valentine's name had changed, written over it was Clary's rune; her name.

"What the hell have you done? My daughter?" Valentine roared, looking Clary in the eyes.

For the first time Clary saw the depraved, twisted, power hungry man that was her father.

The angel Raziel sent a bright light piercing through Valentine's heart, effectively ending his life. The angel then came over to Clary and lifted the bindings off of her, giving her mobility and voice back.

"You have summoned me, Daughter of Valentine, what is it you desire?" The angel's voice was like thunder.

Clary looked over at her brother, she couldn't voice her desire. Would the angel leave her, disgusted, if she asked to die with her brother? Clary looked back at the angel with bright eyes to find him looking at Jonathan. Raziel walked over and placed a bright light over Jonathan's heart, then walked back to the lake and disappeared.

Clary felt disappointment enter her entire being, she flopped back on her back; too tired to try and crawl back to her brother. She was overcome with darkness and let herself drift there for a long time.

A voice was calling her name.

A beautiful voice was calling her name and a hand was stroking her hair out of her face.

She didn't want to open her eyes, was she hallucinating? Did the angel actually grant her wish to be with her brother?

Slowly she opened her eyes.

He was above her, looking down upon her.

With bright green eyes not unlike her own.

**Part 2**

Yesterday was Clary's twentieth birthday, Jonathan had given her a beautiful locket with a picture of them inside. He looked proud as he handed it to her, smiling mischievously. Their little hidden cottage in Alicante was decorated with bright balloons and streamers. Jonathan had then seen fit to escort her to their mother's house for a quick visit.

Things were tense with their mother but they were trying. They did keep their relationship from her, didn't openly flaunt it but they had a feeling she knew. After the death of Valentine, Jonathan had taken Jocelyn back to the institute; and together Magnus Bane and a man name Lucian woke her. Lucian was apparently an old friend who had been searching for Jocelyn for years, never giving up hope on the woman he loved.

They now lived together in New York.

Luke had a book store and Jocelyn an art studio.

Clary's relationship with her mother came easier than Jonathan's but he didn't begrudge Clary the opportunities to visit.

The Clave had agreed to leave Clary and Jonathan alone, after all they did to stop Valentine. It also helped that they were still technically children at the time and had been raised by a psycho path, how were they supposed to understand what they had done was wrong when it was all they had ever known? There was a timid agreement that as long as they stayed off of the Clave's radar, the Clave would stay off of theirs. Although a couple of members were very interested in Clary's talent with runes. A terrifying glare from Jonathan convinced them to drop the subject.

The Clave was working on reforming some accords with downworlders and some laws.

They were also pruning their ranks, trying to weed out the corrupt members.

Jace had taken Clary aside, about a week after it was all over and she was still at the institute, and explained that while he did not completely understand her relationship with Jonathan he wouldn't judge her for it. He had seen the way Jonathan had reacted when they figured out, with help from Magnus, that Valentine had taken Clary. "He went batshit insane." He had said. Jace had also noticed the way that the siblings looked at each other.

Jace was still a Shadow Hunter.

One of the best that ever was or will be.

The Lightwoods had been let free of the institute, since they had been on the Clave's side this time around. Isabelle, Robert, Max, and Maryse went on a month long trip to Paris to celebrate while Alex moved in with Magnus. Apparently he and Magnus had become something of an item but that was still a secret from the Clave.

Magnus and Alex couldn't be happier.

Isabelle sadly died while on a mission at a vampire party.

Robert and Maryse took Max to Idris after that.

They came back to the institute last year and reunited with Jace.

Clary never saw them but Luke was still on good terms with the Lightwoods and Magnus and when she went to visit Jocelyn he kept her up to date.

There wasn't a single day that went by that Clary missed her father, instead she felt at peace. She and Jonathan were now free to be themselves, and while they lived in Alicante they killed demons at night.

The death of Valentine didn't just bring peace to her but his death and Raziel brought peace to Jonathan. Jonathan no longer had deep dark black eyes, they now had the same eyes. Their mother's eyes. That wasn't the only thing that changed, his temper had calmed considerably and he was in much higher spirits. He wasn't as fast, strong, or agile as he had once been but he was still one of the best Shadow Hunters.

Clary suspected that Raziel had rid Jonathan of the demon in him and returned him to the person he should have been; had it not been for Valentine's interference. Clary had been worried at first; that with the change in his blood his feelings for her would change as well, but that worry had quickly been abolished. At the very first opportunity that they had alone, he completely ravished her. Telling her how much he loved her over and over again.

He told her almost daily that he was amazed her desire had been him, out of anything in the world. It brought him back to life.

Thank Raziel.

She told him almost daily that all she had ever wanted was him.

When they had talked about their future, Clary had expressed her concern that he would eventually be bitter. They could never have kids, it would just be them until the day that they died. Would he resent never being able to have a family?

Promptly he got down on one knee and produced a beautiful diamond ring, old fashioned but perfect.

"All I need is you," He had said. "All I want is you."

Just you.

**End.**


End file.
